rs1407709

Positions:

• chr1-188093548-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000648838.2(ENSG00000285894):​n.455-3591T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.769 in 152,090 control chromosomes in the GnomAD database, including 45,608 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.77 (45608 hom., cov: 31)
• Consequence: ENST00000648838.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.286

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.842 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000648838.2	n.455-3591T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.769 AC: 116812 AN: 151972 Hom.: 45554 Cov.: 31

Gnomad AFR AF: 0.625

Gnomad AMI AF: 0.763

Gnomad AMR AF: 0.821

Gnomad ASJ AF: 0.784

Gnomad EAS AF: 0.863

Gnomad SAS AF: 0.780

Gnomad FIN AF: 0.870

Gnomad MID AF: 0.777

Gnomad NFE AF: 0.819

Gnomad OTH AF: 0.773

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.769 AC: 116922 AN: 152090 Hom.: 45608 Cov.: 31 AF XY: 0.774 AC XY: 57557 AN XY: 74344

Gnomad4 AFR AF: 0.626

Gnomad4 AMR AF: 0.822

Gnomad4 ASJ AF: 0.784

Gnomad4 EAS AF: 0.864

Gnomad4 SAS AF: 0.780

Gnomad4 FIN AF: 0.870

Gnomad4 NFE AF: 0.819

Gnomad4 OTH AF: 0.776

Alfa AF: 0.800 Hom.: 23141

Bravo AF: 0.762

Asia WGS AF: 0.827 AC: 2875 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.7
DANN	Benign	0.75

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1407709; hg19: chr1-188062679;